Contents

Description

This script calculates the true center-of-mass (COM) or the center-of-geometry (COG) for a given selection and returns the x, y, z values in the form of a Pseudoatom (rather than a CGO sphere). The benefit of using a Pseudoatom is that it can be selected and used in calculations. In addition, this script also iteratively goes through all states of a selection if more than one state exists and appends the corresponding COM/COG values as states into the Pseudoatom. The script itself is quite simple yet robust enough to be applied in different settings. As well, the calculation of the COM/COG is handled independently from the formation of the Pseudoatom and can be called as an independent function where applicable.

Usage

com selection [,state=None[,mass=None[,object=None]]]

Examples

import center_of_mass
fetch 1c3y, finish=1, multiplex=0
com 1c3y, state=1#Create a pseudoatom representing the 1c3y COG and store it as "1c3y_COM"#The "1c3y_COM" object will contain 1 state only
com 1c3y, state=1,object=COG
#Create a pseudoatom representing the 1c3y COG and store it as "COG"#The "COG" object will contain 1 state only
com 1c3y, state=1,object=COM, mass=1#Create a pseudoatom representing the 1c3y COM and store it as "COM"#The "COM" object will contain 1 state only
com 1c3y,object=COM, mass=1#Create a single pseudoatom containing the COM for each state found in 1c3y and store it as "COM"#The "COM" object will contain MULTIPLE states!